Abstract
Before designing a synthetic promoter, it can be helpful to think about its final application. Is the study purely an in vitro exercise in monitoring short-term promoter activity from an episomal vector, or does the promoter eventually need to be permanently active and be integrated into the genome or perhaps even to function in vivo? The final application will have a bearing on promoter design and vector of choice from the start of the study. In this chapter I highlight some of the vector attributes to consider and features that should be thought about.
References
Grieger JC, Samulski RJ (2005) Packaging capacity of adeno-associated virus serotypes: impact of larger genomes on infectivity and postentry steps. J Virol 79:9933–9944
Wu J, Zhao W, Zhong L, Han Z, Li B, Ma W, Weigel-Kelley KA, Warrington KH, Srivastava A (2007) Self-complementary recombinant adeno-associated viral vectors: packaging capacity and the role of rep proteins in vector purity. Hum Gene Ther 18:171–182
Maelandsmo GM, Ross PJ, Pavliv M, Meulenbroek RA, Evelegh C, Muruve DA, Graham FL, Parks RJ (2005) Use of a murine secreted alkaline phosphatase as a non-immunogenic reporter gene in mice. J Gene Med 7:307–315
Shimizu N, Miura Y, Sakamoto Y, Tsutsui K (2001) Plasmids with a mammalian replication origin and a matrix attachment region initiate the event similar to gene amplification . Cancer Res 61:6987–6990
Levitt N, Briggs D, Gil A, Proudfoot NJ (1989) Definition of an efficient synthetic poly(A) site. Genes Dev 3:1019–1025
SF Y, von Ruden T, Kantoff PW, Garber C, Seiberg M, Ruther U, Anderson WF, Wagner EF, Gilboa E (1986) Self-inactivating retroviral vectors designed for transfer of whole genes into mammalian cells. Proc Natl Acad Sci U S A 83:3194–3198
Zufferey R, Dull T, Mandel RJ, Bukovsky A, Quiroz D, Naldini L, Trono D (1998) Self-inactivating lentivirus vector for safe and efficient in vivo gene delivery. J Virol 72:9873–9880
Mohamed H, Chernajovsky Y, Gould D (2016) Assembly PCR synthesis of optimally designed, compact, multi-responsive promoters suited to gene therapy application. Sci Rep 6:29388
Chung JH, Bell AC, Felsenfeld G (1997) Characterization of the chicken beta-globin insulator. Proc Natl Acad Sci U S A 94:575–580
Bell AC, West AG, Felsenfeld G (1999) The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98:387–396
Baiker A, Maercker C, Piechaczek C, Schmidt SB, Bode J, Benham C, Lipps HJ (2000) Mitotic stability of an episomal vector containing a human scaffold/matrix-attached region is provided by association with nuclear matrix. Nat Cell Biol 2:182–184
Piechaczek C, Fetzer C, Baiker A, Bode J, Lipps HJ (1999) A vector based on the SV40 origin of replication and chromosomal S/MARs replicates episomally in CHO cells. Nucleic Acids Res 27:426–428
Verghese SC, Goloviznina NA, Skinner AM, Lipps HJ, Kurre P (2014) S/MAR sequence confers long-term mitotic stability on non-integrating lentiviral vector episomes without selection. Nucleic Acids Res 42:e53
Muller-Kuller U, Ackermann M, Kolodziej S, Brendel C, Fritsch J, Lachmann N, Kunkel H, Lausen J, Schambach A, Moritz T et al (2015) A minimal ubiquitous chromatin opening element (UCOE) effectively prevents silencing of juxtaposed heterologous promoters by epigenetic remodeling in multipotent and pluripotent stem cells. Nucleic Acids Res 43:1577–1592
Subang MC, Fatah R, Wu Y, Hannaman D, Rice J, Evans CF, Chernajovsky Y, Gould D (2015) Effects of APC de-targeting and GAr modification on the duration of luciferase expression from plasmid DNA delivered to skeletal muscle. Curr Gene Ther 15:3–14
Gambotto A, Dworacki G, Cicinnati V, Kenniston T, Steitz J, Tuting T, Robbins PD, DeLeo AB (2000) Immunogenicity of enhanced green fluorescent protein (EGFP) in BALB/c mice: identification of an H2-Kd-restricted CTL epitope. Gene Ther 7:2036–2040
Limberis MP, Bell CL, Wilson JM (2009) Identification of the murine firefly luciferase-specific CD8 T-cell epitopes. Gene Ther 16:441–447
Ginhoux F, Turbant S, Gross DA, Poupiot J, Marais T, Lone Y, Lemonnier FA, Firat H, Perez N, Danos O et al (2004) HLA-A*0201-restricted cytolytic responses to the rtTA transactivator dominant and cryptic epitopes compromise transgene expression induced by the tetracycline on system. Mol Ther 10:279–289
Cornelie S, Hoebeke J, Schacht AM, Bertin B, Vicogne J, Capron M, Riveau G (2004) Direct evidence that toll-like receptor 9 (TLR9) functionally binds plasmid DNA by specific cytosine-phosphate-guanine motif recognition. J Biol Chem 279:15124–15129
Agudo J, Ruzo A, Kitur K, Sachidanandam R, Blander JM, Brown BD (2012) A TLR and non-TLR mediated innate response to lentiviruses restricts hepatocyte entry and can be ameliorated by pharmacological blockade. Mol Ther 20:2257–2267
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Gould, D. (2017). Initial Considerations Before Designing a Promoter Construct. In: Gould, D. (eds) Mammalian Synthetic Promoters. Methods in Molecular Biology, vol 1651. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-7223-4_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7223-4_1
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-7221-0
Online ISBN: 978-1-4939-7223-4
eBook Packages: Springer Protocols